Cheminformatics proving ground

Library synthesizer

Update March 2, 2013: The complete code to this tool is available here.
Library enumeration and profiling are an integral part of a medicinal chemist's repertoire during early-stage discovery. Whether it's synthesis planning for lead optimization or library design for lead identification, having an effective tool to enumerate and profile virtual compounds is ultimately critical to the success of a therapeutic campaign. Library synthesizer is a tool that we recently, working together with a medicinal chemist, develop to address such needs. While the tool is still a work in progress, it's functional to the point that we thought others might find it useful. Clearly, the potential of this tool is limited only by the imagination (and of course implementation), so we'd love to get feedback.
(A note on the implementation: Due to technical difficulties, we weren't able to deploy library synthesizer within the Java web start sandbox like other tools available on this site. This means that, upon launching the tool, you'll be asked to allow an untrust application access to your system. Here, please take our words that it's safe to say yes!)